Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome

This repository contains the trajectory data from "Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome".

Data sets

We provide data sets for the following constructs and imaging conditions, where we give the name of the construct and the MS2-parS genomic separation in kb:

data_line0.csv: parS-homie-evePr-PP7, 58 kb

data_line1.csv: parS-homie-evePr-PP7, 82 kb

data_line2.csv: parS-homie-evePr-PP7, 88 kb

data_line3.csv: parS-homie-evePr-PP7, 149 kb

data_line4.csv: parS-homie-evePr-PP7, 190 kb

data_line5.csv: parS-homie-evePr-PP7, 595 kb

data_line6.csv: parS-homie-evePr-PP7, 3.3 Mb

data_line3_5s.csv: parS-homie-evePr-PP7, 149 kb, 5 second time interval

data_line0_nohomie.csv: parS-lambda-evePr-PP7, 58 kb

data_line3_nohomie.csv: parS-lambda-evePr-PP7, 149 kb

Structure of Data

The trajectory data are provided as csv files consisting of 13 columns. The column headers are:

cell_id: a unique cell index

time_point: the time frame

x_blue: x-coordinate of the locus in the blue channel (units in nm)

y_blue: y-coordinate of the locus in the blue channel (units in nm)

z_blue: z-coordinate of the locus in the blue channel (units in nm)

x_green: x-coordinate of the locus in the green channel (units in nm)  

y_green: y-coordinate of the locus in the green channel (units in nm)

z_green: z-coordinate of the locus in the green channel (units in nm)  

x_Rij: x-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)

y_Rij: y-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)

z_Rij: z-component of the aberration corrected 3D distance vector connecting the blue and green loci (units in nm)

red: intensity in the red channel (a.u.)

state: inferred state using a 3-state HMM, with entries 0 (O_off), 1 (P_off), 2 (P_on)